Until Proven Innocent
by Celtic Knot
Summary: After the events of Mass Effect 2, Alliance NCIS is tasked to investigate Shepard's Cerberus ties. Rating subject to change. On indefinite hiatus, but I'm not giving up yet!
1. Prologue

_Continuity Note: This should remain plausibly canon for Mass Effect, set between 2 and 3. It's AU for NCIS, with Gibbs and his dream team (circa Season 13) set in the Mass Effect timeline._

 _Why? Because my husband and I are total nerds, and this is the kind of thing we talk about on date night. :)_

 **Until Proven Innocent**

 _Prologue_

"Come on, Leon. We're supposed to haul in the greatest hero the Alliance has ever had?"

"The brass wants a full investigation." Alliance NCIS director Leon Vance leaned toward his best agent, bracing his hands on his desk. "She worked for _Cerberus,_ Gibbs."

Special Agent Leroy Jethro Gibbs gave a disbelieving half-smile. "She saved all our asses. You know it, the brass knows it—hell, even the Council knows it. She _used_ Cerberus, and then turned the ship over to the Alliance when she was done! She did what none of them had the balls to do, and they want to accuse her of _terrorism?"_

Vance pushed away from his desk and straightened. "You want to clear Commander Shepard's name, Gibbs? Then do what you do best: _find the truth."_

* * *

The rest of the team was just as incredulous. "But… she's a Spectre," Timothy McGee protested. "Don't Spectres have immunity against this sort of thing?"

"She's also an officer of the Alliance Navy, McGee," Gibbs snapped. "Subject to all the regs that come with the position. Just because the Council won't prosecute her doesn't mean the Alliance can't."

"Boss, they can't be serious." Anthony DiNozzo echoed McGee's disbelief.

"Oh, they're serious." Eleanor Bishop looked up from her computer terminal. "It's all over the extranet already. Shepard's been relieved of duty and placed under house arrest pending our investigation!"

"Can they do that?" asked McGee.

"Looks like they just did." Gibbs settled in at his desk. "DiNozzo, Bishop, go get her and bring her to the conference room for questioning."

DiNozzo stared for a moment, then muttered, "Bring in Rhiannon Shepard, right." He tossed the skycar keys into the air and caught them with a sarcastic, toothy grin. "Ready for a suicide mission of our own, Bishop?"

She followed him out, shaking her head in a gesture that clearly said, _Here goes nothing._

Gibbs turned to the team's tech expert. "McGee."

"Get locations on the rest of the crew. On it, boss."

"And convince them to talk to us. More than half of them are alien nationals," Gibbs reminded him. "Appeal to their loyalty to Shepard. They followed her through the Omega-4 relay; hopefully they'll answer a few questions."

McGee was already typing at his terminal. "I've got contacts on Thessia who can get us in touch with Samara, the justicar. If anybody's word concerning Commander Shepard carries any weight, hers will."

Gibbs nodded. "Good. Go talk to her."

* * *

The crew dossiers were dizzying, the mission reports staggering. With no body to examine (thankfully, considering what had happened to those unfortunate enough to fall victim to the Collectors), Dr. Donald "Ducky" Mallard had plenty of time to put his forensic psychology skills to use. And it would take every ounce of it to make sense of Commander Shepard's squad.

Five humans, six aliens, and a geth, most with colorfully checkered pasts. Almost all of them fiercely independent individuals, and few with any loyalty to the Systems Alliance, they comprised what had to be the most ragtag collection of scoundrels and misfits in the entire annals of military history. And yet they'd followed Shepard into the very maw of hell, with little hope of return.

Zaeed Massani, mercenary. Co-founder of the Blue Suns, nursing a twenty-year vendetta against his former partner.

Legion, geth mobile platform. _Enough said._ And yet not nearly enough.

Tali'Zorah vas Normandy, quarian machinist. Daughter of the late Admiral Rael'Zorah vas Rayya, charged with treason against the Migrant Fleet and later cleared. Named for Shepard's vessel rather than one of the flotilla's.

Dr. Mordin Solus, salarian physician, former STG. Worked on modifications to the genophage that was decimating the krogan population.

Garrus Vakarian, turian, former C-Sec officer. Briefly held the somewhat melodramatic moniker Archangel while leading a squad of vigilantes on Omega. Betrayed by one of his own.

Miranda Lawson, high-level Cerberus commander. Oversaw Project Lazarus, responsible for bringing Shepard back from the dead.

Jacob Taylor, Cerberus operative. Former Alliance officer, father later discovered to be unstable.

Samara, asari justicar. Tasked with hunting down and killing her own daughter, a rogue Ardat-Yakshi.

Urdnot Grunt, krogan warrior. Grown in a tank, genetically engineered to be "perfect."

Thane Krios, drell assassin. Dying of Kepral's Syndrome, and rumored to be romantically involved with Commander Shepard.

Jack, AKA Jacqueline Nought, AKA Subject Zero, self-described "psychotic biotic." Victim of some of Cerberus's most brutal experiments before breaking out of the Teltin facility. Extremely powerful biotic abilities, prone to violence.

Kasumi Goto, master thief. Lover killed for sensitive information contained in his graybox.

Ducky shook his head. Yes, all of these people had followed Shepard on her famous suicide mission. They had fought well and bravely. They deserved as much credit as she did for saving the galaxy once again. And then they had abandoned her, almost to a man, once their contracts with Cerberus were complete. Leaving her to face the Alliance music alone.

He couldn't imagine how these people could help Shepard's case at all.


	2. Chapter 1: Shepard

_Chapter 1: Shepard_

Rhiannon Shepard found herself sympathizing with the mad prophet in the alleys of Omega, ranting to anyone who passed, ignored by most, taken seriously by precious few. The Reapers were coming. She and her crew had slowed them down, but hadn't stopped them. But no one with any clout believed her. No one was preparing. She found herself spending more and more time at the big picture window, staring up at the sky, expecting at any moment to see tentacled starships descending on the city.

That was where the NCIS agents had found her. She didn't turn around to greet them; had simply called out "It's open," when they'd knocked and announced themselves. She kept her back turned, eyes on the sky, and waited for them to state their business.

"Commander, I'm Special Agent Anthony DiNozzo, NCIS; this is Agent Bishop." She could see his reflection in the window, could see him flashing his ID and badge uselessly at her back. Or maybe he was counting on the same reflection. "We'd like you to come with us."

"It's not 'Commander' anymore," Shepard said. Her voice fell toneless even on her own ears. "Am I under arrest?"

DiNozzo's voice was sincere as he replied, "You'll always be _Commander_ Shepard to us at NCIS, ma'am."

"We just want to talk to you," Bishop said gently.

Shepard finally turned around and fixed them both with a weary gaze. "What's there to talk about that I haven't been over already?"

The two agents exchanged a glance. They were an odd-looking pair—where DiNozzo was tall, dark-haired, and a little too impeccably groomed, Bishop was small and blonde, with a fresh-scrubbed kind of cuteness that made her look impossibly young. "We were hoping you would help us find your crew," said DiNozzo.

Whatever inclination Shepard may have had to cooperate with them vanished. "No," she snapped with a sudden fire that brought both agents up short. "I convinced them to leave before I turned over the _Normandy_ specifically so they wouldn't face any of this political bullshit. They worked for me, not for Cerberus. They were my _friends._ I won't help you run them in."

"We're trying to help you, Commander," Bishop blurted out.

Shepard's hands balled into fists and she grimaced, furious and despondent all at once. She'd been prepared to take whatever the Alliance wanted to throw at her, secure in the knowledge that her crew was safe from backlash. But now, even that small reassurance was slipping away. "And just how the hell is arresting my crew supposed to _help_ me?" she demanded.

DiNozzo raised his hands in a placating gesture. "We just want to talk to them, that's all."

"Yeah. You keep saying that." Shepard folded her arms. "But I know better than to think that 'talk' means anything but 'interrogate,' so the answer is still no."

DiNozzo gritted his absurdly perfect teeth in frustration. "Look, Commander, I really don't want to have to do this the hard way. We're on your side here. Why don't you come back to NCIS with us and at least hear us out?"

Shepard opened her mouth to fire back another retort—and closed it again. She would accomplish nothing by fighting with NCIS. Less than nothing. It would only make her look worse, and her chances of being taken seriously would suffer even more. Earth would be a sitting duck for the Reapers. "Fine," she sighed. "Then I'll decide how much I'll tell you about my crew."

* * *

 _This is why you should never meet your heroes,_ DiNozzo thought as he followed Gibbs into the conference room. The first thing he'd noticed when laying eyes on the great Commander Rhiannon Shepard in person had been how small she was. Barely taller than Bishop and just as slender, her delicate frame belied the feats of military prowess she'd accomplished. The news vids had always made her look… well, larger than life. And seeing her out of uniform, in blue jeans and a black N7 hoodie, just seemed wrong, somehow.

Then she'd spoken, and the note of defeat in her voice had further shattered the illusion. Shepard in the vids was always self-assured and confident of victory. Even in the face of that reporter Khalisah bint Sinan al-Jilani's attempts to smear her name and question her motives, she'd maintained a grace and dignity that DiNozzo had rarely seen in anyone but Gibbs. But Shepard in person was just _tired,_ careworn and quick to anger. A burnt-out, broken shell of what had once been a legend. Those emerald eyes that could bore into you with such fire through a vid screen were now cold and dead, staring accusingly at the two agents as they approached.

She'd been watching out the window again.

Now, she stood at a modified parade rest, apparently out of habit, radiating the defiance of a woman with nothing to lose. But she was hollow, on the verge of crumbling, with the weight of the galaxy crushing down on her narrow shoulders. One wrong step and she might buckle. And yet she'd pushed away all those who might have shared the burden with her.

"Commander Shepard, I'm Special Agent Gibbs. You've met Agent DiNozzo." Gibbs gestured to the large table that dominated the room. "Have a seat. Can I get you anything? Coffee?"

Shepard eyed Gibbs suspiciously as she sat down. "No, thanks."

"Suit yourself," Gibbs said with a shrug, taking a seat opposite her. DiNozzo sat beside him, laying a thick file folder on the table. "Let's get straight to the point. Why Cerberus, Commander?"

Shepard sighed wearily. "As I've explained a hundred times already, it was the only way to accomplish the mission. Cerberus gave me a ship, resources, a crew, and oh yeah, _literally brought me back from the dead._ So I took full advantage of everything I had at my disposal to stop the Collectors and slow down the Reapers. And then I _gave it all to the Alliance when I was done."_ She leaned forward and bit out icily, "So tell me this, Agent Gibbs, since apparently nobody else can: besides flying Cerberus colors, what have I done wrong?"

"Nothing." DiNozzo watched, suppressing a smile, as Gibbs gazed levelly at a flabbergasted Shepard. "You acted fully within your authority as a Spectre. That was never in question."

She slammed a fist into the tabletop. _"Then why am I—"_

"Your loyalty to the Alliance was."

That took all the newfound wind out of Shepard's sails, and she slumped back in her seat, mouth agape. A dozen emotions flashed across her face as she processed the implications of that statement. "Agent Gibbs," she said finally, plaintively, _"everything_ I did was for the Alliance."

"I know that. But all the brass has to go on are your mission reports—reports you wrote for the Illusive Man." Gibbs tapped the folder in front of DiNozzo. "They want corroboration."

Understanding dawned on Shepard's face. "That's why you want to talk to my crew." She shook her head sadly. "I can tell you where I dropped each of them off, but they've probably scattered to all corners of the galaxy by now. I haven't heard from any of them in months. Not even…" She trailed off, looking away as tears threatened in her eyes. "I don't know if they'll cooperate. I don't even know if they're all still alive."

"Give us what you can, and we'll find them," DiNozzo reassured her. "We could probably pass along a few messages, too, if you want."

Wide green eyes suddenly held the faintest glimmer of hope. "Just one, Agent DiNozzo."


End file.
